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Thread: R1b-L21 Phylogeny (SNP based family tree)

  1. #61
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    Quote Originally Posted by Mikewww View Post
    Subtopic: Submitting candidate SNPs for placement on ISOGG tree
    It may be worth including the tests used for each SNP, both positive and negative, in the ISOGG submission. Typically, ISOGG has required both positive and negative SNP tests to be confirmed by Sanger sequencing, which can generate considerable extra expense. However, perhaps results obtained by other methods may now be considered on a case by case basis.

    For example, CTS9881, which is positive in the Irish Type 4 subclade of L1066, has recently been added to the ISOGG Y-tree. As it is a new terminal SNP, it was necessary to demonstrate that it is downstream from L1066 and satisfies the GD requirement for ISOGG listing. We had two positive results, one from Geno 2.0 and one from Chromo 2, separated by an appropriate GD. Only one of these has been confirmed by Sanger sequencing. There were multiple negative results in L1066+ persons who were not Irish Type 4, obtained from both Geno 2.0 and Chromo 2 results, but not Sanger testing.

    ISOGG accepted these results, probably because of several factors, including the concordant results between Geno 2.0 and Chromo 2, the large number of negative results (at least twelve) in L1066+ persons (which effectively eliminated any concern regarding no-calls or technical errors), and the correlation between the positive results and an already well-defined (by STRs) grouping. No further Sanger testing was required.

    As there will probably be a large number of new SNPs requiring submission to ISOGG, it may be worth considering what Sanger confirmation is required in each case, and if necessary requesting clarification from ISOGG. I think Mark Jost, the ISOGG co-ordinator for L21, is going to become very busy.

    Greg H

  2. #62
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    Quote Originally Posted by Mikewww View Post
    Subtopic: Submitting candidate SNPs for placement on ISOGG tree


    ----------- Subject line of email --------------------------
    SNP xyz (candidate SNP) Submission for ISOGG tree


    ----------- Outline format of body of email -------------------------


    Candidate SNP and synonym labels
    ----------------------------------------------
    SNP labels, URL to physical address info

    Candidate SNP diversity status
    ------------------------------------------
    Kit #, Surname, Project URL, candidate SNP derived result, Genetic Distance from comparison
    Kit #, Surname, Project URL, candidate SNP derived result (for comparison target)

    Immediate Ancestor (father) SNP currently on ISOGG chart
    ------------------------------------------------------------------
    SNP

    Ancestral and derived haplotypes proving descendant status
    ------------------------------------------------------------------------------
    Kit #, Surname, Project URL, ancestor SNP derived result, candidate SNP deriived result
    Kit #, Surname, Project URL, ancestor SNP derived result, candidate SNP ancestral result

    Peer (brother) SNP currently on ISOGG chart (1 through n) (if applicable)
    -----------------------------------------------------------------
    Kit #, Surname, Project URL, peer SNP derived result, candidate SNP ancestral result

    Descendant (child) SNP currently on ISOGG chart (1 through n) (if applicable)
    -----------------------------------------------------------------
    Kit #, Surname, Project URL, descendant SNP derived result, candidate SNP derived result
    Kit #, Surname, Project URL, descendant SNP ancestral result, candidate SNP derived result
    Here is a table of a summary of ISOGG qualification that I have used at my L21 web site. With so many duplicate
    YSNPs with Full YChr tests, we need to post those YSNPs as well.



    SNP
    Number
    FTDNA Submission Number
    (or WTY GRC number)
    Project Name Test Results
    Prove ISOGG Father of DF73
    DF73+
    58625
    L21 Plus
    Z2534+
    Prove DF73 is not a duplicate of Z2534
    DF73-
    77349
    L21 Plus
    Z2534+
    Eliminate possible fathers of DF73
    DF73+
    58625
    L21 Plus
    L226-
    DF73+
    58625
    L21 Plus
    L643-
    DF73+
    58625
    L21 Plus
    Z2185-
    Eliminate possible sons of DF73
    DF73-
    77349
    L21 Plus
    L226+
    DF73-
    57521
    L21 Plus
    L643+
    DF73-
    231060
    L21 Nat Geo
    Z2185+
    Prove duplicate SNPs of DF73
    NA
    None known
    NA
    NA
    Prove SNPs that are sons of DF73
    NA
    None known
    NA
    NA
    Prove 10 % Diversity (ISOGG)
    DF73+
    58625
    L21 Plus
    Base
    DF73+
    143916
    L21 Plus
    GD=16


    Of course, a Project URL may not be a FTDNA YSNP report. It could be Big Y file, FG file, Nat Geo file, Walk the Y file, CROMO2, YSEQ, etc. I am not
    sure that Surname will ever be required but it does enhance the information as YSNPs get genealogical - yet still make the GD qualification. I think
    that duplicate YSNPs need to be separated from private sons - this is a major improvement in the ISOGG haplotree for tracking proven private sons
    that do not yet qualify for the diversity requirement vs. just lumping them into duplicates. This would be much better improvement than surnames.
    Last edited by RobertCasey; 02-25-2014 at 03:59 PM.

  3. #63
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    Quote Originally Posted by RobertCasey View Post
    ....
    Of course, a Project URL may not be a FTDNA YSNP report. It could be Big Y file, FG file, Nat Geo file, Walk the Y file, CROMO2, YSEQ, etc.
    Agreed. I just think there needs to be some link to a public testing institution web site so the authority standing behind the test result is confirmed.

    Quote Originally Posted by RobertCasey View Post
    .... I am not sure that Surname will ever be required but it does enhance the information as YSNPs get genealogical - yet still make the GD qualification.
    I don't think it is required. I added it as a checkpoint with the kit#/ID#. I've found that is always good to include a name with the ID as occasionally digits get transposed.

    Quote Originally Posted by RobertCasey View Post
    . I think
    that duplicate YSNPs need to be separated from private sons - this is a major improvement in the ISOGG haplotree for tracking proven private sons
    that do not yet qualify for the diversity requirement vs. just lumping them into duplicates. This would be much better improvement than surnames.
    I'm not sure I'm following you completely on this.

    The format I suggested does not really support phylogenetically equivalent SNPs. I just want to get something on board for positioning/insertion of newly discovered SNPs. Equivalent SNPs are another matter that is one of gray areas. SNPs are artificially deemed equivalent at some point but I don't know of a minimum testing requirement.

  4. #64
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    Quote Originally Posted by Mikewww View Post

    I'm not sure I'm following you completely on this.

    The format I suggested does not really support phylogenetically equivalent SNPs. I just want to get something on board for positioning/insertion of newly discovered SNPs. Equivalent SNPs are another matter that is one of gray areas. SNPs are artificially deemed equivalent at some point but I don't know of a minimum testing requirement.
    I agree that a URL link is key (citing source references is always desirable). I agree that adding surname would help - but this is unlikely to fly with ISOGG.

    As far as equivalent YSNPs, ISOGG does accept these and posts hundreds of them. We should continue to submit known equivalent YSNPs. I am thinking about adding Z252 as an equivalent of Z253. I think this adds value to the haplotree for older equivalents so people do not continue discover it is an equivalent. There are around ten 1K tests and two FG tests that indicate that Z252 is equivalent of Z253 as well as many other L21 tests that indicate Z252 is not between Z253 and L21. Maybe there should be a separate form for older equivalents. Sorting the equivalents out is a major task that should be documented - at least for older YSNPs that have descendants. ISOGG is the best place to track all the different names of the same mutation as well as all those equivalents as well.

    As far as "private" YSNPs under terminal YSNPs, I think ISOGG needs to at least track them in some manner - but like surnames, that is unlikely. I think this would a enormous improvement to add a list equivalents (similar to how Thomas Krahn listed many YSNPs as approximate to YSNPs). They may proven as sons or ancestors to the approximate YSNP later - but the ISOGG haplotree could provide a great place to put those thousands of YSNPs that are under research.
    Last edited by RobertCasey; 02-25-2014 at 06:20 PM.

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    Quote Originally Posted by RobertCasey View Post
    I agree that a URL link is key (citing source references is always desirable). I agree that adding surname would help - but this is unlikely to fly with ISOGG..
    I'm not advocating adding surnames to the ISOGG trees or anything like that... although that would be interesting to think about in the future with much better phylo tree mapping technologies (hopefully).

    I'm only asking ISOGG for guidance on how they want to see submissions for branch creating SNP insertions into tree.

    Quote Originally Posted by RobertCasey View Post
    As far as equivalent YSNPs, ISOGG does accept these and posts hundreds of them. We should continue to submit known equivalent YSNPs. I am thinking about adding Z252 as an equivalent of Z253. I think this adds value to the haplotree for older equivalents so people do not continue discover it is an equivalent. There are around ten 1K tests and two FG tests that indicate that Z252 is equivalent of Z253 as well as many other L21 tests that indicate Z252 is not between Z253 and L21. Maybe there should be a separate form for older equivalents. Sorting the equivalents out is a major task that should be documented - at least for older YSNPs that have descendants. ISOGG is the best place to track all the different names of the same mutation as well as all those equivalents as well.
    I agree that equivalent SNPs must be considered and need to be added to the tree. I just didn't have that as a first priority vis a vis SNP insertion/branch creation. I'm a little unclear on the definition of when equivalency can be assumed. Obviously duplicate testing (duplicate of the original branch marking SNP) across peers and children is required depending on the situation. However how many Lead with SNP + Equivalent SNP + and - - results are needed to assume equivalency is something I don't know. Making the equivalency assumption is a game of probabilities but can only be truly understood in hindsight.

    Quote Originally Posted by RobertCasey View Post
    As far as "private" YSNPs under terminal YSNPs, I think ISOGG needs to at least track them in some manner - but like surnames, that is unlikely. I think this would a enormous improvement to add a list equivalents (similar to how Thomas Krahn listed many YSNPs as approximate to YSNPs). They may proven as sons or ancestors to the approximate YSNP later - but the ISOGG haplotree could provide a great place to put those thousands of YSNPs that are under research.
    Private SNPs may be the most important of all and it is mind boggling to manage in a broad way. I think every youthful subclade needs its own advocate.

    L21xDF13xDF63
    DF63
    DF13xBig10
    DF49xM222
    M222
    DF21
    DF41
    L513
    L1335
    CTS4466
    Z251
    Z253
    Z255
    FGC5496
    ... more to come.

    BTW, I think Mark J is our L21 ISOGG coordinator. May God bless him!

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    Quote Originally Posted by hoxgi View Post
    It may be worth including the tests used for each SNP, both positive and negative, in the ISOGG submission. Typically, ISOGG has required both positive and negative SNP tests to be confirmed by Sanger sequencing, which can generate considerable extra expense. However, perhaps results obtained by other methods may now be considered on a case by case basis.

    For example, CTS9881, which is positive in the Irish Type 4 subclade of L1066, has recently been added to the ISOGG Y-tree. As it is a new terminal SNP, it was necessary to demonstrate that it is downstream from L1066 and satisfies the GD requirement for ISOGG listing. We had two positive results, one from Geno 2.0 and one from Chromo 2, separated by an appropriate GD. Only one of these has been confirmed by Sanger sequencing. There were multiple negative results in L1066+ persons who were not Irish Type 4, obtained from both Geno 2.0 and Chromo 2 results, but not Sanger testing.

    ISOGG accepted these results, probably because of several factors, including the concordant results between Geno 2.0 and Chromo 2, the large number of negative results (at least twelve) in L1066+ persons (which effectively eliminated any concern regarding no-calls or technical errors), and the correlation between the positive results and an already well-defined (by STRs) grouping. No further Sanger testing was required.

    As there will probably be a large number of new SNPs requiring submission to ISOGG, it may be worth considering what Sanger confirmation is required in each case, and if necessary requesting clarification from ISOGG. I think Mark Jost, the ISOGG co-ordinator for L21, is going to become very busy.

    Greg H
    We have seen that the Geno2/Chromo2 technology level produced some strange results and in some cases many no calls. Supposedly, Big Y (and I would think FGC hi-quality results) are supposed to have a more accurate and reliable testing. I don't know if that is true, but if it is that could change things.

    We've seen on other threads that Warwick has proposed that it may not be economic to run one at a time Sanger Sequencing for all candidate SNPs.

    I don't know, but I think the conservative approach, which Mark J has advocated, is the Sanger Sequencing validation. That would make Thomas Krahn/YSEQ happy. I've got my sample "in the mail" to them with hopes of having some stuff to "make a wish" for and have one at a time testing options. I have our L21 data (STRs and SNPs) integrated through YSEQ's ID=11 R1b-L21 public display.

  7. #67
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    Quote Originally Posted by Mikewww View Post
    BTW, I think Mark J is our L21 ISOGG coordinator. May God bless him!
    ISOGG Notes section says
    Changed R1b-P312 contact person to Mark Jost on 6 February 2014.
    Not just L21, that is.

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    Quote Originally Posted by razyn View Post
    ISOGG Notes section says "P312"

    Not just L21, that is.
    He needs a double or triple dose of favor then.

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    Just an update. I'm NOT updating the R1b-L21_Tree_Chart powerpoint, .png and .pdf files for the time being. There is just too much change to try to worry about drawing it up manually as things shift. The new Chromo 2 anonymized file has been very helpful but we don't know have a clear view into the identities and haplotypes as well as how those SNPs (phylogenetically) relate to new FGC and Big Y identified SNPs. I'll update the graphical trees, but not for a while.

    Several people are doing great work on analyzing information. I am convinced this needs to be done at lower and lower (more youthful) levels of the tree taking us down to DF13's big ten subclades, DF13* and DF63's subsclades and then even more youthful into the genetic genealogy realm.

    I think there is a huge point of leverage with the 340 plus Big Y results we will see for L21. This gives us a good and consistent scan of the Y chromosome (what FTDNA calls the "gold" regions). What's important is that sets up for a nice apples to apples comparison which is what is needed for phylogenetic tree identification (comparative methods - click here.)

    That being said, I'm working on what I call R1b-L21_SNP_Tree_Discovery. This file is a quick view of all 104 (so far but will go up to 350) L21 derived variants from the "gold" regions. This file can be access from the R1b-L21-project yahoo group. There is a have a classification system for SNPs (i.e. single individual, single surname, multi-family, public consistent, public unsure, etc.) I include STR signature variety labels for individuals. In some cases the variety labels are being destroyed, but usually they are validated. Eventually, people at 111 STRs should be able to get a good idea of what SNPs they want to test for if they want to do a one at a time (a la carte) approach.

    After I'm done with that, I'll review all derived simple SNPs (straight allele one for one changes) by individual in a comparison. This won't be apples to apples but sets up for inclusion of comparisons with other test packages, including reverse engineering one at a time SNP results from FTDNA and YSEQ or Geno 2 and Chromo 2 where people are sharing their data.

    Anyway, it goes without saying. If you are L21+, join the R L21 project. Join other pertinent projects but the L21 project is a very large database in and of itself so that is the best place (IMO) for up to date info. Plus... Richard S is the fastest haplogroup project administrator around.

  10. The Following 4 Users Say Thank You to TigerMW For This Useful Post:

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    I'll try to cross-post here (from the L21 yahoo group) when get breaks.

    Here is an update - Are DF41 and Z255 brothers under super-subclade of DF13?

    This variant is not named but it is consistent from a phylogenetic standpoint so far (everything is always "so far".)
    16132308T>TGATA

    It appears in all 7 Z255 guys and 3 of 6 DF41 guys. The other 95 L21 Big Y folks don't have it reported as derived.

    I checked the .vcf files on the other 3 DF41 guys that don't have it. That location is not in those file so we don't know if they have it or don't. It's possible then, that 16132308T>TGATA indicates DF41 and Z255 are brothers.

    Z255 is not that old and it is related to L159.2 (not sure exactly how, though). The Irish Sea/Leinster/Lagin STR varieties people are the biggest part of it.

    DF41 has a few different signatures some of which may be Welsh and some of which may be Scottish and other Breton. I'm sure some are Irish too and something else in the British Isles.
    Last edited by TigerMW; 03-28-2014 at 06:59 PM.

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